# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 12:48:54 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: 4-(pyridin-2-yl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc(cc1)c2ccccn2
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 PQS  PQS  '4-(pyridin-2-yl)benzoic acid'  ligand  23  15  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PQS
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 PQS  C10  C  CR6    0  -0.107   2.3346   0.0081   0.0163
 PQS  C11  C  CR16   0  -0.275   1.5959  -1.1517  -0.2069
 PQS  C12  C  CR16   0  -0.276   0.2109  -1.1324  -0.1975
 PQS  C13  C  C      0   0.397   3.8581  -0.0179   0.0097
 PQS  C01  C  CR16   0  -0.151  -4.0720   1.1779  -0.2350
 PQS  C02  C  CR16   0  -0.339  -2.6884   1.2272  -0.2509
 PQS  C03  C  CR6    0   0.224  -1.9634   0.0673   0.0281
 PQS  C05  C  CR16   0  -0.074  -3.8974  -1.1286   0.3010
 PQS  C06  C  CR16   0  -0.328  -4.6994  -0.0250   0.0508
 PQS  C07  C  CR6    0   0.067  -0.4847   0.0567   0.0277
 PQS  C08  C  CR16   0  -0.309   0.2540   1.2186   0.2556
 PQS  C09  C  CR16   0  -0.272   1.6396   1.1915   0.2498
 PQS  N04  N  N      0  -0.427  -2.5730  -1.0889   0.2916
 PQS  O14  O  O      0  -0.592   4.3954  -1.1273  -0.1703
 PQS  O15  O  OC    -1  -0.592   4.4347   1.0722   0.1857
 PQS  H1   H  HCR6   0   0.244   2.1130  -2.0834  -0.3951
 PQS  H2   H  HCR6   0   0.245  -0.3404  -2.0461  -0.3772
 PQS  H5   H  HCR6   0   0.261  -4.3472  -2.0906   0.5215
 PQS  H6   H  HCR6   0   0.271  -5.7765  -0.1131   0.0737
 PQS  H7   H  HCR6   0   0.247  -0.2493   2.1547   0.4637
 PQS  H8   H  HCR6   0   0.245   2.1894   2.1039   0.4395
 PQS  H3   H  HCR6   0   0.274  -4.6506   2.0660  -0.4529
 PQS  H4   H  HCR6   0   0.269  -2.1839   2.1512  -0.4971

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 PQS  O14  C13  deloc     1.246  0.020  1.246
 PQS  C13  O15  deloc     1.246  0.020  1.246
 PQS  C13  C10  single    1.524  0.020  1.524
 PQS  C09  C10  aromatic  1.392  0.020  1.392
 PQS  C09  C08  aromatic  1.386  0.020  1.386
 PQS  C10  C11  aromatic  1.393  0.020  1.393
 PQS  C08  C07  aromatic  1.396  0.020  1.396
 PQS  C11  C12  aromatic  1.385  0.020  1.385
 PQS  C07  C12  aromatic  1.396  0.020  1.396
 PQS  C07  C03  single    1.479  0.020  1.479
 PQS  N04  C05  aromatic  1.325  0.020  1.325
 PQS  N04  C03  aromatic  1.333  0.020  1.333
 PQS  C05  C06  aromatic  1.387  0.020  1.387
 PQS  C03  C02  aromatic  1.396  0.020  1.396
 PQS  C02  C01  aromatic  1.385  0.020  1.385
 PQS  C06  C01  aromatic  1.386  0.020  1.386
 PQS  C11  H1   single    0.930  0.020  1.080
 PQS  C12  H2   single    0.930  0.020  1.080
 PQS  C01  H3   single    0.930  0.020  1.080
 PQS  C02  H4   single    0.930  0.020  1.080
 PQS  C05  H5   single    0.930  0.020  1.080
 PQS  C06  H6   single    0.930  0.020  1.080
 PQS  C08  H7   single    0.930  0.020  1.080
 PQS  C09  H8   single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 PQS  C09  C10  C13  120.96  3.000
 PQS  C09  C10  C11  118.03  3.000
 PQS  C13  C10  C11  121.02  3.000
 PQS  H1   C11  C12  119.40  3.000
 PQS  H1   C11  C10  119.43  3.000
 PQS  C12  C11  C10  121.17  3.000
 PQS  H2   C12  C07  119.48  3.000
 PQS  H2   C12  C11  119.77  3.000
 PQS  C07  C12  C11  120.74  3.000
 PQS  O15  C13  O14  126.88  3.000
 PQS  O15  C13  C10  116.57  3.000
 PQS  O14  C13  C10  116.55  3.000
 PQS  H3   C01  C06  120.77  3.000
 PQS  H3   C01  C02  120.18  3.000
 PQS  C06  C01  C02  119.04  3.000
 PQS  H4   C02  C03  120.88  3.000
 PQS  H4   C02  C01  119.96  3.000
 PQS  C03  C02  C01  119.15  3.000
 PQS  N04  C03  C07  116.82  3.000
 PQS  N04  C03  C02  121.50  3.000
 PQS  C07  C03  C02  121.68  3.000
 PQS  H5   C05  N04  116.26  3.000
 PQS  H5   C05  C06  120.18  3.000
 PQS  N04  C05  C06  123.56  3.000
 PQS  H6   C06  C05  120.50  3.000
 PQS  H6   C06  C01  121.73  3.000
 PQS  C05  C06  C01  117.77  3.000
 PQS  C08  C07  C03  121.56  3.000
 PQS  C03  C07  C12  120.29  3.000
 PQS  C08  C07  C12  118.15  3.000
 PQS  H7   C08  C09  118.84  3.000
 PQS  H7   C08  C07  120.33  3.000
 PQS  C09  C08  C07  120.81  3.000
 PQS  H8   C09  C08  119.39  3.000
 PQS  H8   C09  C10  119.51  3.000
 PQS  C08  C09  C10  121.09  3.000
 PQS  C05  N04  C03  118.97  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 PQS  CONST_01  C07  C08  C09  C10    0.00   0.0  0
 PQS  CONST_02  C07  C12  C11  C10    0.00   0.0  0
 PQS  CONST_03  C08  C09  C10  C11    0.00   0.0  0
 PQS  CONST_04  C08  C07  C12  C11    0.00   0.0  0
 PQS  CONST_05  C03  C07  C12  C11  180.00   0.0  0
 PQS  CONST_06  C09  C10  C11  C12    0.00   0.0  0
 PQS  CONST_07  C09  C08  C07  C12    0.00   0.0  0
 PQS  CONST_10  C07  C03  C02  C01  180.00   0.0  0
 PQS  CONST_11  N04  C03  C02  C01    0.00   0.0  0
 PQS  CONST_12  N04  C05  C06  C01    0.00   0.0  0
 PQS  CONST_14  C05  N04  C03  C02    0.00   0.0  0
 PQS  CONST_15  C05  C06  C01  C02    0.00   0.0  0
 PQS  CONST_16  C09  C08  C07  C03  180.00   0.0  0
 PQS  CONST_17  C06  C05  N04  C03    0.00   0.0  0
 PQS  CONST_18  C06  C01  C02  C03    0.00   0.0  0
 PQS  CONST_19  C07  C03  N04  C05  180.00   0.0  0
 PQS  CONST_21  C13  C10  C11  C12  180.00   0.0  0
 PQS  CONST_22  C08  C09  C10  C13  180.00   0.0  0
 PQS  CONST_23  H7   C08  C09  C10  180.00   0.0  0
 PQS  CONST_24  H2   C12  C11  C10  180.00   0.0  0
 PQS  CONST_25  H8   C09  C10  C11  180.00   0.0  0
 PQS  CONST_26  H5   C05  C06  C01  180.00   0.0  0
 PQS  CONST_27  H6   C06  C01  C02  180.00   0.0  0
 PQS  CONST_28  H3   C01  C02  C03  180.00   0.0  0
 PQS  CONST_29  H4   C02  C01  C06  180.00   0.0  0
 PQS  CONST_30  H1   C11  C12  C07  180.00   0.0  0
 PQS  Var_01    O14  C13  C10  C11   -1.76  30.0  2

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 PQS  plan-1  C10  0.020
 PQS  plan-1  C11  0.020
 PQS  plan-1  C12  0.020
 PQS  plan-1  C13  0.020
 PQS  plan-1  C03  0.020
 PQS  plan-1  C07  0.020
 PQS  plan-1  C08  0.020
 PQS  plan-1  C09  0.020
 PQS  plan-1  H1   0.020
 PQS  plan-1  H2   0.020
 PQS  plan-1  H7   0.020
 PQS  plan-1  H8   0.020
 PQS  plan-2  C01  0.020
 PQS  plan-2  C02  0.020
 PQS  plan-2  C03  0.020
 PQS  plan-2  C05  0.020
 PQS  plan-2  C06  0.020
 PQS  plan-2  C07  0.020
 PQS  plan-2  N04  0.020
 PQS  plan-2  H5   0.020
 PQS  plan-2  H6   0.020
 PQS  plan-2  H3   0.020
 PQS  plan-2  H4   0.020
 PQS  plan-3  C10  0.020
 PQS  plan-3  C13  0.020
 PQS  plan-3  O14  0.020
 PQS  plan-3  O15  0.020

